Mercurial > repos > ieguinoa > data_manager_fetch_tx2gene
comparison data_manager/data_manager_fetch_tx2gene.xml @ 4:bacd91d8b05a draft
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| author | ieguinoa |
|---|---|
| date | Sun, 21 Oct 2018 17:48:48 -0400 |
| parents | d71f65b854de |
| children |
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| 3:d71f65b854de | 4:bacd91d8b05a |
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| 1 <tool id="data_manager_fetch_tx2gene" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data"> | 1 <tool id="data_manager_fetch_tx2gene" name="Create entries in tx2gene data table" version="0.0.1" tool_type="manage_data"> |
| 2 <description>fetching</description> | 2 <description>fetching</description> |
| 3 <requirements> | 3 <requirements> |
| 4 <requirement type="package" version="1.26.4">bioconductor-genomicfeatures</requirement> | 4 <requirement type="package" version="1.32.3">bioconductor-genomicfeatures</requirement> |
| 5 <requirement type="package">r-getopt</requirement> | 5 <requirement type="package">r-getopt</requirement> |
| 6 </requirements> | 6 </requirements> |
| 7 | 7 |
| 8 <command><![CDATA[ | 8 <command><![CDATA[ |
| 9 python "$__tool_directory__"/data_manager_fetch_tx2gene.py "${out_file}" | 9 python "$__tool_directory__"/data_manager_fetch_tx2gene.py "${out_file}" |
| 16 | 16 |
| 17 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> | 17 <param name="dbkey" type="genomebuild" label="DBKEY to assign to data" /> |
| 18 <param type="text" name="sequence_name" value="" label="Name of sequence" /> | 18 <param type="text" name="sequence_name" value="" label="Name of sequence" /> |
| 19 <param type="text" name="sequence_id" value="" label="ID for sequence" /> | 19 <param type="text" name="sequence_id" value="" label="ID for sequence" /> |
| 20 | 20 |
| 21 <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)"> | 21 <param name="file_type" type="select" label="Select input type: GFF/GTF file(features will be extracted to create tx2gene table) or transcript to gene table file(tab separated)" help="When using GFF3/GTF files as input, transcript feaatures must contain a transcript_id attribute."> |
| 22 <option value="gtf">GTF file</option> | 22 <option value="gtf">GTF file</option> |
| 23 <option value="gff3">GFF3 file</option> | 23 <option value="gff3">GFF3 file</option> |
| 24 <option value="tx2gene">tx2gene</option> | 24 <option value="tx2gene">tx2gene</option> |
| 25 </param> | 25 </param> |
| 26 <conditional name="reference_source"> | 26 <conditional name="reference_source"> |
| 58 </test> | 58 </test> |
| 59 </tests> | 59 </tests> |
| 60 <help> | 60 <help> |
| 61 **What it does** | 61 **What it does** |
| 62 | 62 |
| 63 Fetches a gff file from various sources (URL, Galaxy History, or a server directory) and populates the "all_gff" data table. | 63 Populate the tx2gene data table with transcript-genes mapping tables. |
| 64 | 64 |
| 65 ------ | 65 ------ |
| 66 | 66 |
| 67 | 67 |
| 68 | 68 |